The present dataset contains the abundance data (ind. m-3) of total mesozooplankton, main groups and copepod species from the Long Term Ecological Research station MareChiara in the Gulf of Naples (st. LTER-MC, 40°48.5’ N, 14°15’ E) over the years 1984-2015. Zooplankton samples were collected by vertical tows in the upper 50 m using an Indian Ocean net (200-µm mesh, 113-cm mouth diameter) and fixed with buffered formaldehyde (2–4% final concentration). In the laboratory, the samples were concentrated and resuspended in filtered seawater to a volume of 200 ml to remove the formaldehyde. Aliquots ranging from 1/4 to 1/32, according to the sample density, were initially taken using the Huntsman beaker subsampling technique and successively with a large-bore graduated pipette after careful mixing. Aliquots were transferred to a mini-Bogorov chamber (10 ml) and examined under a stereomicroscope and all zooplankton taxa were identified and counted. The entire sample was checked for the presence of rare species. The copepod abundances reported here correspond to the whole population (adult females and males, and copepodites).